PTCD2

pentatricopeptide repeat domain 2, the group of Pentatricopeptide repeat containing

Basic information

Region (hg38): 5:72320367-72368395

Links

ENSG00000049883

∙ NCBI:79810 ∙ OMIM:615484 ∙ HGNC:25734 ∙ Uniprot:Q8WV60 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PTCD2 gene.

not_specified (50 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTCD2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024754.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			47 clinvar	3 clinvar		50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	47	3	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTCD2	protein_coding	protein_coding	ENST00000380639	10	39859

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.13e-11	0.135	125677	0	71	125748	0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.128	196	201	0.975	0.00000968	2543
Missense in Polyphen		33	44.557	0.74062		604
Synonymous	-0.750	88	79.5	1.11	0.00000403	733
Loss of Function	0.503	17	19.4	0.877	9.19e-7	260

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000931	0.000929
Ashkenazi Jewish	0.00	0.00
East Asian	0.000385	0.000381
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000204	0.000202
Middle Eastern	0.000385	0.000381
South Asian	0.000362	0.000359
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Involved in mitochondrial RNA maturation and mitochondrial respiratory chain function. {ECO:0000250}.;

Intolerance Scores

loftool: 0.695
rvis_EVS: -0.65
rvis_percentile_EVS: 16.36

Haploinsufficiency Scores

pHI: 0.0276
hipred: N
hipred_score: 0.144
ghis: 0.560

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.246

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Ptcd2
Phenotype: liver/biliary system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); renal/urinary system phenotype; muscle phenotype; cellular phenotype;

Gene ontology

Biological process: kidney development;liver development;mRNA processing;mitochondrion organization;muscle fiber development;regulation of mRNA processing;ventricular cardiac muscle tissue morphogenesis
Cellular component: mitochondrion
Molecular function: RNA binding